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- PDB-9c9e: Crystal structure of fluoroacetate dehalogenase 4A from Delftia a... -

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Basic information

Entry
Database: PDB / ID: 9c9e
TitleCrystal structure of fluoroacetate dehalogenase 4A from Delftia acidovorans strain D4B
ComponentsFluoroacetate dehalogenase 4A
KeywordsTRANSFERASE / Dehalogenase PFAS
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.585 Å
AuthorsCaputo, A.T. / Hu, M. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: To Be Published
Title: Crystal structures of two fluoroacetate dehalogenases
Authors: Hu, M. / Caputo, A.T. / Scott, C.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4613
Polymers26,3291
Non-polymers1322
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.225, 68.496, 69.909
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fluoroacetate dehalogenase 4A


Mass: 26329.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Strain: D4B / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8 mg/ml A4, 2 M Ammonium sulfate, 2% (v/v) PEG400, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.585→48.926 Å / Num. obs: 27201 / % possible obs: 94.2 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rpim(I) all: 0.052 / Net I/σ(I): 7.8
Reflection shellResolution: 1.585→1.612 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1302 / CC1/2: 0.528 / Rpim(I) all: 1.748

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data processing
Aimless0.7.9data scaling
PHASER2.8.3phasing
XDSJan 10, 2022 (BUILT 20220220)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.585→48.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1349 -RANDOM
Rwork0.2256 ---
obs0.2266 26822 92.9 %-
Displacement parametersBiso mean: 27.37 Å2
Baniso -1Baniso -2Baniso -3
1-8.827 Å20 Å20 Å2
2--1.9322 Å20 Å2
3----10.7592 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.585→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 6 123 1741
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093207HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15761HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d932SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes522HARMONIC5
X-RAY DIFFRACTIONt_it1667HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion202SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2540SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion14.43
LS refinement shellResolution: 1.585→1.6 Å
RfactorNum. reflection% reflection
Rfree0.4593 26 -
Rwork0.4118 --
obs--70.27 %

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